non-integer numReads for differential expression analysis

Question

[Sam]

Dear All

I want to find predicted lncRNA expression according to RNA-seq data, I prepared a database from all of the predicted lncRNA and then I aligned the PE RNA-seq libs to the indexed lncRNA db via salmon. but in salmon output files there is some non-integer numReads, what is the best approach to handle this non-integer numbers for DE analysis. Thanks

    Name    Length  EffectiveLength TPM NumReads
CUFF.47.1   1011    845.627 21.0942 250.461
CUFF.53.2   734 570.457 45.1108 361.328
CUFF.54.1   760 596.362 87.4186 732
CUFF.57.1   825 661.123 268.776 2495
CUFF.58.2   338 176.503 356.296 883
CUFF.80.1   1348    1182.63 0.594387    9.86994

[ATpoint]

Hello Sam!

We believe that this post does not fit the main topic of this site.

Please use google first. Question has been asked multiple times.

See here for a comment of the DESeq2 developer.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[Sam]

I don't have gft file for my db, in that case can I use the tximport ?

[ATpoint]

Please read the manual at Bioconductor for the tximport package. You do not need a GTF.